tophat install problem

Question

[biolab]

Hi everyone

I installed boost (prefixed at /data/xma/local/boost/), bowtie, samtools, all without problem, but am facing tophat problem:

checking whether Boost::Thread needs Boost::System library... configure: error: Cannot use Boost::Thread

My command is

./configure \
  --prefix=/data/xma/local/tophat/ \
  --with-boost=/data/xma/local/boost/ \
  --with-bam=/data/xma/tools/samtools-0.1.19

I tried adding the option --with-boost-libdir=/data/xma/local/boost/lib, unfortunately it does not work. Could anyone kindly offers me solutions? I have been in trouble for hours. Thanks a lot!

[biolab]

I finally resolved the problem. The --with-boost option is wrong, should be --with-boost=/data/xma/local/boost/include/boost/. Hope this post helps in case anyone else meet the same problem.

Answer 1

[mmfansler]

Ran in to exactly the same error, but neither of the above were the issue for me. Perhaps unique to the fact that I have boost installed through macports, my system only has libboost_system-mt in the lib directory and was not being recognized. Adding a soft link for libboost_system in the same directory was all I needed. Was smooth sailing from there on out.

[cagolino]

Thank you!!!! This perfectly fixed my issue.

Answer 2

[Philipp Bayer]

Hello,

I just ran into the same issue with tophat, but the above solution didn't work for me.

./configure --prefix=path/to/install --with-boost=boost/base/dir/

(boost/base/dir needs to include two directories - include and lib)

For me, tophat's small example script at configure's line 5558 to test for Boost:Thread didn't work properly (in the step "checking whether Boost::Thread needs Boost::System library..."), here's the error message from the logs (you can get the logs in "config.log" with ./configure --enable-debug)

thread.cpp:(.text+0xdb): undefined reference to `clock_gettime'

In the configure script, I had to change this line

CXXFLAGS="-pthread $CXXFLAGS"

to

CXXFLAGS="-pthread -lrt $CXXFLAGS"

Using the -lrt flag adds the "Real Time" library to compilation, which adds that missing method.

I also had to add -lrt to src/Makefile in CXXFLAGS

Then, running make produced the correct binaries. It seems to differ between systems. I'd recommend to always use the pre-compiled binaries.